Yes, I would bet the milk may have been to acidic to get a clean break. I really like frankhouser, but I have to say sometimes I find his instructions a bit difficult to interpret. I was never sure if "overnight" meant 4 hours, 5 hours, 8 hours, 10 hours, or if it just didn't matter.
Also, I'd really check your rennet. I'm not sure the brand/type you used, but I know at least some animal rennets loose their potency after 6 months. Just for the sake of experimentation you might try using a different rennet, such as Junket tablets which can be found at places like walmart (in the ice cream topping area normally).
Good luck!